


The Chronicles of Mewtwo Mini Series

by Dominod18



Category: Pocket Monsters | Pokemon (Anime), Pocket Monsters | Pokemon (Main Video Game Series), Pocket Monsters | Pokemon - All Media Types
Genre: Multi
Language: English
Status: Completed
Published: 2020-05-18
Updated: 2020-05-18
Packaged: 2021-03-03 00:21:32
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence
Chapters: 1
Words: 18,008
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/24245704
Author URL: https://archiveofourown.org/users/Dominod18/pseuds/Dominod18
Summary: There is a scene in the very first Pokemon movie that was cut because it was too tragic for younger audiences.  It's when Mewtwo is just an infant and makes a friend with a dying young girl named Amber Fuji, the daughter of the man who created Mewtwo.  In the original story, Amber doesn't survive and Mewtwo's memory is wiped in order not to be dramatized by the event.  As a result, Mewtwo suffers from a feeling of loss and has no idea why which leads Mewtwo to a severe case of identity crisis and leads to the events of the first movie.  But what if in an alternate story, Amber survives.That's what this fan-fiction is all about, where Amber survives and Mewtwo has a friend.  But it's not all sunshine and flowers as Team Rocket's Leader: Giovanni help funds the research that created Mewtwo and he wants his Pokemon back.
Comments: 5
Kudos: 3





	The Chronicles of Mewtwo Mini Series

www.johnathanposhea.wordpress.com/art/

Open the link to see the story as a movie script. This is how I write my stories. Let me know if you are having problems trying to open this pdf.

But just in case you can’t, here it is condensed.

Amber Fuji dies in a car accident, Dr. Fuji is devastated by this loss. During the funeral, he meets Giovanni who can bring her back. In return, Giovanni wants him to create a clone of Mew and has a fossil to achieve this. Mrs. Fuji is against this and divorces Dr. Fuji. He goes to the lab to bring Amber back and create the Pokemon called Mewtwo. During the cloning process, Mewtwo and Amber communicate with each other and become friends. However, Amber dies and Mewtwo erupts in anger, wrecking the lab in the process.

Mewtwo finds Amber’s lifeless body, he heals and revives her. Amber is alive and reunited with her dad. Mewtwo demands that he stays with Amber and can reunite Mrs. Fuji. They flee to Pallet Town just as Giovanni arrives at the lab. Giovanni sends Team Rocket to search for Mewtwo, but they can't find this Pokemon.

The Fuji’s are reunited and Mewtwo is adopted into the family. They change their names to Toshi and lie low in Pallet Town. Dr. Fuji, now Mr. Toshi, gets a job working for Professor Oak as an assistant and they take Mewtwo in to analyze the Pokemon. Turns out Mewtwo is insanely powerful and wants to start training to perfect its power. The reason why is Mewtwo and Amber want to go on a Pokemon journey. The parents are against the idea out of fear that Team Rocket will catch them and separate them. Mewtwo promises not to fight them in order to fool them that Mewtwo is weak. Convinced by this, they agree to let him and Amber go on their journey. But first, they need money.

Dr. Fuji tries to get a loan from the bank, but the bank denies to offer. Mewtwo comes up with a plan to rig the upcoming Pokemon championship in their favor and win the betting money to fund their journey. Hiding in the ceiling overlooking the stadium, Mewtwo aids a young Pokemon trainer named Ash Ketchem to win with the use of some subtle psychic tricky. This lets Ash win and the Fuji’s just won a huge jackpot of money. Little did they know that Team Rocket tracks all the league’s money and the Fuji family is exposed. Mewtwo returns home and helps Amber pack her bag for the journey. He heads to Pallet Labs to get some training done before they start leaving and everyone sleeps peacefully that night.

The next morning, as Mewtwo meditates in an isolated chamber, the Fuji’s are attacked by James, Jesse, Butch, Cassidy, and Meowth of Team Rocket. They demand the whereabouts of Mewtwo, they tell them but they refuse to surrender and fight back, only to be gunned down by Butch and Cassidy. They clean up any empty bullet cases they find and burn the house down, making it look like a tragic accident rather than a murder. Mewtwo returns home only to find ashes and dead bodies. Mewtwo is devastated by this loss. Ash Ketchem returns by bus to find his neighbor’s house completely destroyed and a Pokemon in tears. He and his friends, Misty and Brock, take him back to Pallet Labs. End of part 1.

Part 2 opens with a flashback to with a ten-year-old Amber in Cyro-tube slowly being healed next to a baby Mewtwo also in a Cryo-tube. Dr. Fuji is there trying to convince his wife that what he is doing isn't crazy, that Amber can and will come back. Mrs. Fuji believes that her husband is crazy and leaves him. Inside Amber's mind, she is alone surrounded in darkness and she is scared. She is then introduced to baby Mewtwo who is also lost and scared. More so because Mewtwo can't remember its past. The two of them agree to stick together and try to find a way out of the darkness.

It has been two days since the Fuji Family died and Mewtwo is still grieving. Only a slightly burnt photo of the family remains from the fire. Mewtwo now lives with Professor Oak at the lab. Oak returns from the funeral to find Mewtwo alone in the lab holding the photo. When asked why Mewtwo did go to the funeral, it replied with saying goodbye again would simply be much to handle. Just then, a lawyer comes in to tell The Pokémon that it became the sole inheritor of the family’s life insurance money and the federal government has agreed to make Mewtwo a free citizen, meaning no Pokémon Trainer is allowed to capture this Pokémon. Professor Oak has allowed Mewtwo to stay and be his assistant in the lab. 

Flashback to the lab where Mewtwo was created, when we see Giovanni and Dr. Fuji analyzing a Ditto. Ditto is a failed Mew clone and Giovanni is not impressed. Then Dr. Fuji shows Giovanni Mewtwo still growing in the chamber next to Amber. Dr. Fuji warns Giovanni that Mewtwo could most likely die if not fully developed. Giovanni agrees and gives the doctor more time for Mewtwo to grow. Meanwhile, Amber and baby Mewtwo hear voices in the darkness. This frightens Mewtwo to the point of holding Amber like a child clinging to its mother. Amber comforts the scared Pokémon and they talk about angels. This talk helps calm Mewtwo as they continue through the darkness.

Cut to present day where it has been three days since Amber’s death, where Mewtwo is visited by a visitor in the night. It’s Amber, only she is a ghost and she is in tears. Mewtwo follows her back to the house that burned down three days ago. Amber tells Mewtwo everything that happened and that they died protecting Mewtwo from Team Rocket. They have a tearful embrace before Amber disappears back to the heavens, leaving Mewtwo alone. Mewtwo punches the burnt floor in a bit of tearful rage, only to be interrupted by a clanging sound. A brass bullet casing popped out from the ash. Mewtwo now knows it wasn’t seeing things, it saw Amber and she cannot rest until justice is done. Mewtwo crushes the casing with its psychic power and vows revenge on Team Rocket and Giovanni. Mewtwo rushes back to the lab, just in time to miss Butch and Cassidy who were about to confront the angry Pokémon. Back at the lab, Mewtwo gathers supplies for a journey to hunt down and destroy Team Rocket. Using its psychic powers, it crafts a cloak from its bedsheets, it grabs a satchel and fills it with a few snack goods, empty Pokeballs, a Pokeball with Scyther in it, the family photo, and some cash. Mewtwo leaves without telling the Professor where it’s going or even saying goodbye. Butch and Cassidy see Mewtwo fly off in the night sky and warn the rest of Team Rocket that Mewtwo is out.

Flashback to Dr. Fuji being frustrated with Mewtwo’s slow development. This is nothing more than angry muffled sounds in the darkness that Amber and Mewtwo and this alarm them. Then Mewtwo sees something peering through the darkness. It's a Squirtle, a Bulbasaur, and a Charmander with unique patterns on their bodies. Amber assures Mewtwo that these are Pokemon and that they are harmless. Mewtwo can understand what they are saying and Amber gets the idea to have Mewtwo ask them where they are and how do they get out of the darkness. 

Cut back to present day where Mewtwo looks down at a busy city from the highest building. Mewtwo is in Fuschia City looking for Team Rocket when it hears a cry for help. Mewtwo goes to investigate. Turns out it's a member of Team Rocket steal a Pokeball from someone, Mewtwo stops the thief and returns the Pokeball to its rightful owner. It then forces the Team Rocket Grunt to show it where the base is after Mewtwo tortures to information out of him. 

In an underground tavern, Team Rocket uses this bar as the main hideout. They turned it into a private bar when four Pokemon work there and they have to put up with their rude behavior. The Pokemon are Duke, the Machamp; Simon, the Chandlure; Erica, the Lopunny; and Lexi, the Infernape. They are the bouncer, DJ, waitress, and bartender respectively. Erica gets the worst treatment from her human guests, but she and the others need this job because nowhere else will hire them for work. As Duke is about to kick some Team Rocket members out of the bar for harassing Erica, a Team Rocket member is hurled into the bar, crashing into Duke. The member is dead and Duke gets a bump on the head. Then the door to the bar is locked by a mysterious figure wearing a cloak. This figure demands the whereabouts of Giovanni and threats to kill everyone who doesn't comply. All Team Rocket members pull out their guns and open fire. They miss. Turns out this cloaked figure is Mewtwo, and he just dodged every bullet at point-blank range. Then with a psychic burst of energy, he pushes all members to the floor. Mewtwo summons two shadow balls and demands the whereabouts of Giovanni.

Duke and Simon try to stop Mewtwo, but the shadow balls knock them out cold. Erica and Lexi hide behind the bar as Mewtwo begins the slaughter. In the chaos, the fire sprinkler system goes off and one by one, Mewtwo slays Team Rocket without mercy. Then one member, fearing for her life, tells the location of one of Cassidy. After receiving the information, Mewtwo gives her a quick death, then brutally murders the rest of them. Erica turns off the sprinkler system and begs Mewtwo to spare them. Mewtwo informs the scared Erica that he has no business killing Pokemon, just the humans who murdered his family. Lexi brings out a shotgun from under the counter and demands Mewtwo to leave. She lowers her guard once Mewtwo revives both Duke and Simon. Lexi then gets an idea to use Mewtwo as a means to overthrow the human race and convinces her friends they should join Mewtwo. At first, they hesitate, Pokemon who go rogue ends up dead. But their mood shifts when Mewtwo reveals a secret in the broom closet. A secret passage leading to an underground tunnel system and a young human boy named Tommy chained to a wall. He was abused and taken from his family. The four Pokemon realize that Team Rocket isn't a sports club like they were told, it's a secret crime syndicate lead by Giovanni and none of them know where he is, but they have a lead. The Pokemon free Tommy and promise to bring him home. Mewtwo uses teleport on Tommy, the Pokemon in the bar and himself out of the bar.

As the police arrive, they use a Machoke to pry open the door. What the find is a massacre. Meanwhile, the Pokemon gather their belongings at their rundown apartment and soon teleported to the Pokemon Reservation. There Mewtwo heals Tommy of his wounds. Mewtwo then informs his new team that he can only teleport to places he been to in the past. Teleporting out of the bar just brought them to the outside of the city. Tommy lives in Celedon City, Mewtwo can only fly himself and others to a new location. Then Lexi warms Mewtwo that she is afraid of heights. Mewtwo uses his psychic powers to put her in a deep sleep. With that problem solved, Mewtwo flies himself and his new friends into the air and flies off to Celedon City. End of Part 2.

On the way to Celedon City, Lexi wakes up from her sleep put on by Mewtwo and freaks out. She is airborne along with her friends thanks to Mewtwo’s power. Mewtwo says they are almost to the location where Tommy lives, Lexi covers her eyes for the rest of the trip due to her fear of heights. They arrive at a mansion where Tommy lives and are greeted by a Mr. Mime who is a butler for the mansion and close friend of Tommy. Mewtwo and his new friends are welcomed in as Tommy and his Mom are reunited. They are rewarded with a place to stay and another reward in the morning. 

Meanwhile, police investigate the crime scene left behind by Mewtwo. They use an Alakazam named Xavier to read the minds of the dead humans, but that is difficult as memories fade when the brain rots. Still, Xavier does discover these victims are not innocent. Nearly all Pokemon here are stolen which raises questions about the killings here and the motive. Xavier does find out through mind reading a corpse who the killer was, Mewtwo. Xavier finds his info using Officer Jenny’s Pokedex. But just as Xavier gets on the trial, the commissioner takes over the investigation seemingly out of nowhere.

The next day, as everyone wakes up from a long night, Mewtwo has a dream of him and Amber on their Pokemon journey. Amber is shot by Team Rocket and a talking Meowth mocks Mewtwo just before he gets shot. He wakes up in terror. Lexi is there to see what is the matter after having a hot shower. She sees a photo in Mewtwo’s satchel and finds that it's a family photo of him and the humans who adopted him. Lexi is saddened to see this, she then informs Mewtwo that he is welcome to stay with her and the others when all this is over. They head to the dining area of the mansion to find a huge brunch waiting for them. 

Meanwhile, Giovanni receives word from the commissioner of Fuschia City that all Team Rocket members were brutally murdered. No Pokemon were killed there so he and Giovanni send a warrant out for the arrest of Mewtwo and the Pokemon that are with him. Back at the mansion, the Pokemon are enjoying their meal. And the host is a former gym leader named Beth and she wants to know how five Pokemon were able to find her long lost son. Mewtwo claims it was by accident and that Tommy was one of many children and Pokemon taken by Team Rocket and held for ransom. Mewtwo then asks to use a phone to call Professor Oak to inform him of the situation. During their talk, Mewtwo gets angry when he learns that Oak doesn't support Mewtwo’s quest for revenge and begins to storm out of the mansion. Simon tries to stop him but fails. It's not until Tommy stops him that he calms down and gives the young boy a goodbye hug. Beth then writes a check to Mewtwo worth so much that the other Pokemon faint from seeing the value of the check. Beth assures them that it was worth it just to get her son back and sends them on their way. The Pokemon led by Mewtwo take an oath to aid Mewtwo in his revenge quest and put an end to Team Rocket once and for all.

Flashback to Amber and Baby Mewtwo were the young Pokemon becomes scared of the three Kanto Starter Pokemon and holds on to Amber begging to move on. Amber is puzzled as to why Mewtwo is scared of these harmless Pokemon, Mewtwo is fearful for Amber's life and starts freaking out when Bulbasaur gets too close. Amber has had enough and orders Mewtwo to stop being a coward. Mewtwo apologizes to the other Pokemon who hug tackle and snuggle the frightened Mewtwo. Amber calms him by letting him know that they just want to be his friend. As soon as Mewtwo is calm, he asked where they all are. Charmander explains they are in a dream and are completely lucid in this dream. Squirtle them explains that they arrived here to get stronger through gene splicing ( whatever that means ) but all Amber hears is the Pokemon just saying their names over and over again. Mewtwo then tells Amber what was told him. Amber has no memory on how she got here, all she remembers is that she was playing outside near a street, her dad was yelling something to her, then everything went dark. Mewtwo has no memory of his past. But all the Pokemon can hear is ” human, human.” Then Amber suggests that they should have fun while they are still lucid. And that is what they do. On the outside, a scientist working with Dr. Fuji realizes that the brain waves of Amber and the Pokemon are identical. As if Mewtwo is communicating to all of them using its psychic powers. Dr. Fuji feels he and his team are close to seeing these Pokemon wake up on their own, but more importantly, Amber will wake up too.

Flash forward to Celedon City were Mewtwo is holding a Team Rocket member by the throat. He demands the whereabouts of Giovanni but is not getting an answer. Mewtwo reads his mind and finds no leads, then breaks the Rocket member’s neck for calling him worthless. Mewtwo then calls for his next victim. Lexi pulls a young female bartender from out of the broom closet and presents her to Mewtwo. She claims to know nothing and is afraid for her life. Mewtwo promises her no harm if she just cooperates with him. She suggests that Mewtwo just go ahead and read her mind because that's how little she knows. Mewtwo reads her mind, turns out she only got the job a week ago and notice a talking Meowth with a man and a woman dressed in white with a red R on their shirts. They left in a hurry but she did overhear something about looking for a Mew in the Safari Zone. Mewtwo now has a new lead and seeing that this woman is innocent, he uses the move amnesia on her so she would have no memory of what happened here. Mewtwo ’s crew then grab whatever food and drinks they can get and teleport to the Safari Zone. They arrived at a camping lodge, the same one he and the Fuji’s stayed at a few years ago. There, the Pokemon celebrate their victory by getting drunk from all the stolen liquor, Mewtwo just goes to sleep while the others get wasted. 

The next morning, a park ranger goes to inspect the lodge. He doesn't find the Pokemon who stayed there, just a huge mess. Meanwhile, Team Rocket members Jesse, James, and Meowth are searching for rare Pokemon to catch when Meowth spots Mewtwo and crew out in the open. They plan to ambush them. Lexi, Erica, and Duke have sobered up while Simon has a hangover. Mewtwo can't use his healing ability on a ghost type Pokemon but their conversation is distracted by a wild Meowth, or so they thought. Turns out its Meowth from Team Rocket and he was just a distraction while James fires a tear gas grenade at them and traps the Pokemon in smoke. Mewtwo escapes, pulls out a Pokeball and summons Scyther, his former sparring partner. Using his large wings, scyther blows the smoke away. That is when Team Rocket appears with Wobbafett. After reciting to Team Rocket Motto, Mewtwo goes in for the mind-reading, only to be blocked by Wobbafett’s power. Lexi goes in for the attack but is repelled back by Wobbafett. Mewtwo then decides to make a wager. If Mewtwo and his friends lose in a Pokemon battle against Team Rocket, he will surrender. If Team Rocket loses, they must reveal the location of Giovanni. They all agree to this. Jesse summons Arbok, Lickatong, Yenmega, and Gourgiest. While James summons Weezing, Chimcho, Cacnea, and Victrebel. Meowth calls the battle and the Pokemon battle begins. End of part 3.

Part 4 opens with a flashback of the Viridian Forest when Mewtwo hugs a tree out of fear. Amber is there with him and goes sees what spooked him. Turns out it's a baby Caterpie and Amber calls out for being such a coward. She demands Mewtwo to come and pet the Caterpie in order to get over his fear of bug type Pokemon. Mewtwo is afraid of bugs, ghosts, and dark creatures; Amber tells him that if he gets over his fears, he would become the most Pokemon in the world. This gets Mewtwo the idea to continue his training with Pokemon he fears in order to become stronger. Professor Oak agrees to this and he partners him with a Scyther. 

Cut to present day where Mewtwo and his friends are battling the Pokemon owned by Team Rocket where he and Scyther team up to take down Jesse’s Yanmega. Lexi easy defeats Arbok with her close-combat moves, Duke pulverizes Victrebel, Erica beats up Lickitong, Scyther cuts Chimcho down, and Simon burns Weezing, Gourgiest, and Cacnea with a single inferno move. Meanwhile, Mewtwo’s shadow ball bounces off Wobbafett. In his rage, Mewtwo unleashed a barrage of shadow balls onto Wobbafett. So much so, the other Pokemon take cover, and when the dust clears, Team Rocket still stands. But just as their confidence is high, Wobbafett passes out from energy fatigue. Team Rocket is defenseless and retrieves their fallen Pokemon. However, Jesse was secretly gathering new and better Pokemon using her Pokemon trader app on her phone, which allows her to trade Pokemon across the internet with other Team Rocket members. She and James just received a Blaziken and Greninja and they insist the battle isn't over until all Pokemon are defeated. Mewtwo feeling confident he and his team can still win, agrees to let Jesse and James use their new Pokemon for one last round. Blaziken and Greninja come forth and Mewtwo can sense that these two are no pushovers, they completed their training and he realizes his team will be defeated if they attack these Pokemon one on one. So Mewtwo and his friends decide to use a tag-team strategy to win this fight. Lexi is quickly attacked by Blaziken and Greninja bombards the rest with razor-sharp water shurikens, Mewtwo uses his light screen move to shield the others, but Greninja uses his taunt move on Mewtwo, which he falls for and goes for the attack. Greninja uses substitute to dodge Mewtwo’s attack and kicks Mewtwo from the side with a powerful kick straight to the cheek. Knocking Mewtwo out cold. Greninja then goes after Erica and Scyther while Simon and Duke help Lexi. 

Jesse pulls out an ultra ball and throws it at the unconscious Mewtwo, but it's just a trick. Mewtwo was conscious the whole time and using his psychic powers, he crushes the ball and begins to self heal. Erica guards him while he heals up.

Meanwhile Lexi is holding her own against Blaziken despite the fact that she is outclassed compared to Blaziken. Yet she dodges attack after attack and lands in a few punches and kicks here and there. Then Duke comes in to tag Lexi out so he can fight. Duke is much slower and heavier than Lexi so he relies on his grappling to get the job done. But he can't seem to get Blaziken in any kind of finishing move. Simon waits eagerly for his turn.

At the same time, Mewtwo tags Scyther out so he and Greninja and finish their fight. Team Rocket now realizes what Mewtwo and his friends are doing and they pull out their phones to trade more Pokemon. Mewtwo has had enough and shatters their phones and weapons with his psychic powers. However, this leaves Mewtwo wide open for an attack, and Greninja goes in for a fatal blow. Mewtwo is hit with water sword strikes and quick attacks before being hit with a kick so powerful it sends Mewtwo in billboard hundreds of yards away. He crashes through it and collapses on the ground. Everyone is shocked on how strong this Greninja is but Scyther goes in for the attack anyway. 

Mewtwo slowly gets up, heals himself, grabs the giant metal spoon from the broken billboard, and is filled with pure rage. He flies back and savagely beats up Greninja with his weapon and is clearly not holding back anymore. Mewtwo launches Greninja in the air same time as Duke finally grips Blaziken and throws him skyward too. Simon and Scyther beat the injured Pokemon back to earth where Erica bounces out of the way of Greninja only to land hard on his back, causing him to pass out from the pain. Meanwhile, Blaziken lands back first onto Lexi's stiff arm, causing Blaziken to be paralyzed. All but one Pokemon from Team Rocket are defeated and Mewtwo points to the one Pokemon who did not fight this whole time, Meowth. Without hesitation, Meowth surrenders and is brought forth by Mewtwo to be questioned. But rather than waste any more time, he reads Meowth’s mind for the location of Giovanni. Instead, he finds the Fuji Family home being broken into, the family held hostage then murdered by Team Rocket: all from Meowth’s perspective. Mewtwo snaps out of the Psychic link with tears in his eyes. He just saw the death of his family and there was nothing he could do to stop it. He goes from sorrow to rage in the blink of an eye after Moewth said in a pleading manner that he was only doing his job. First Mewtwo slowly squeezes the life out of the helpless Pokemon causing bones to snap, then he repeatedly slams Meowth to the ground again and again and again until Meowth is so broken he can't breathe and is drowning in his own blood. Mewtwo then launches the dying Pokemon right into James’ chest, knocking them both to the ground. Jesse finds herself trapped by Mewtwo’s psychic powers. Jesse is staring down the eyes of a Pokemon intended to kill, fearful for her life she gives the location of Team Rocket’s main base of operations. Giovanni is in Viridian City in the Pokemon Gym. A quick mind read confirms that she is telling the truth. Mewtwo lives up to his end of the bargain and spares their lives, even using his energy to heal and revive Meowth. Mewtwo also claims that he is sparing them because they were there to witness the murder of his family but did not actually kill them. Their hearts are not entirely evil, just misguided. Jesse, James, and Meowth don't wait to leave, as soon as Mewtwo orders them to leave, they run as fast as they can into the forest and out of sight. 

Then Mewtwo remembers a vital clue to his revenge quest, Dr. Fuji gave Mewtwo strict instructions to never go anywhere near Viridian City, now with Jesse’s knowledge he knows why. He was told that the city is evil and now it makes sense, Giovanni lives there and he will pay.

After Mewtwo heals his friends, he reveals the next plan of attack, a flight to Viridian City. Lexi is already scared due to her fear of heights. Mewtwo grabs his cloak, satchel, puts Scyther back in his ball, and takes the giant spoon, and gives Lexi a hug and tells her to only look at him. Then he takes off with the other Pokemon falling behind thanks to his power. 

At first Lexi panics but calms down as they get closer. Mewtwo’s embrace eventually soothes her during the flight. They arrive at the front gate of the Gym and slowly approach the front door. Duke suggests that Mewtwo uses a massive shadow ball to level the whole place and be done with it all. While that would be the easiest solution, Mewtwo points to a wanted poster on a lamp post with all their names on it and suggests capturing the gym with everyone inside and presenting police with enough evidence of Team Rocket’s activities to get their names cleared of the crimes placed on them. Mewtwo then calls out the Giovanni via telepathy and orders the murderer to come out of hiding. Giovanni hears this and demands a Pokemon battle. Mewtwo agrees with the terms being that Giovanni pays for his crimes and his friends cleared of all crimes. The fronts doors revealing Blastoise, Charizard, and Venasaur all with strange markings on them. Mewtwo recognizes these Pokemon as their pre-evolved forms from seven years ago. He and Amber thought they died in the lab, it turns out not only did they survive, but they also became servants of Team Rocket. Mewtwo hopes to reason with them with memories of the past, but these three don't seem to recognize their old friend. Then the Pokemon begin to glow and change into their mega evolved forms. And with one direct hit from Blatoise’s water cannon, Lexi is knocked out cold. Mewtwo and the others realize this fight just got serious. Charizard and Mewtwo fly high for an airborne battle. Erica tries to revive Lexi while Duke tries to wrestle with a Pokemon many times his size. Venasaur charges up for a solar beam attack, an attack that could easily destroy Simon due to being a ghost type Pokemon and his kind are weak to sun based attacks. Mewtwo tries to warn Simon to get out of the way, but Charizard punches Mewtwo back down to earth. Simon is caught off guard by this and Venasaur unleashes a Solar Beam right at Simon, causing his ghostly body to be vaporized in the attack, Simon the Chandelure is no more. Erica and Duke watch in horror to see their friend vanish like that. Mewtwo gets up to see bits of broken glass fall from the sky. He knows what just happened and goes after Venasaur only to be pinned down by Charizard. Blastoise grabs Duke and throws him into the side of the Gym like he weighed nothing, knocking him out cold. As Erica rushed to help Duke, she is caught by Venasaur’s vines and she is slowly being squeezed to death. She screams in pain, which causes Mewtwo to become so angry he taps into a hidden power within him. This causes an explosion of energy blasting Charizard off and land back first on the ground. Mewtwo is enveloped in this aura and his face has a look of pure hatred in his eyes. He flies over and punches Blastoise so hard he flies and crashes into Venasaur and sends them both into the forest just outside the Gym. This causes Erica to fall into Mewtwo’s arms and he begins to heal her. As the three Pokemon come back to confront Mewtwo, he orders Erica to get Scyther out of his Pokeball, grab their things and their wounded friends, and get out of here. He will buy her time.

Erica realizes she had gotten a strength boost so she can carry Lexi and Duke easily and she begins to load their bags and satchels onto Scyther and he flies back to Pallet Town. Just as Erica is about to hop away with a Pokemon in each arm. She gets shot in the back by Team Rocket member Domino, and she collapses to the ground gasping for air. Mewtwo tries to save her but is quickly overpowered by Charizard. Mewtwo is unable to stop Charizard, Blastoise, and Venasaur and is beaten to near death. Domino orders the Pokemon to back off so she can catch Mewtwo for Giovanni with a Master Ball. Erica sees this and tries crawling her way back to Mewtwo only to be pinned by Charizard. Domino throws the ball and hits Mewtwo, causing him to turn into energy and get sucked into the ball. 

Mewtwo wakes up in his old bedroom where Amber is there waiting for him, but Mewtwo is buying this. And turns out that Amber is a Porygon and that Mewtwo is in the Master Ball. And that everything is a simulation programmed to comfort Mewtwo. But he wants out and uses an Aura Sphere to try to blast his way out, only for the Sphere to bounce back and hit Mewtwo, knocking him out. 

The Master Ball stop shaking and the ball finally clicks, indicating that Mewtwo was successfully caught. Erica tears up and cries just as the police arrive. Erica, Lexi, and Duke are taken away by the police as Team Rocket bribes to police to do so and not ask questions. Domino gives the Master Ball to Giovanni and she is given a raise and the rest of the week off. Giovanni stores to Master Ball in a secure briefcase and travels to the nearest Pokemon Center to have Mewtwo healed. 

A few days later, James, Jesse, and Meowth arrive at Giovanni’s office with nervousness on their faces. Giovanni usually gives them grief about failing to turn in Pokemon to him, but it turns out Giovanni is rewarding them. He told them to find and bring Mewtwo to him and technically they did their job. They found Mewtwo and by telling him where Giovanni is, they sent the Pokemon straight to him. James gets a fire stone and gets to keep Greninja. Jesse gets to keep Blaziken and is given a Mimikyu. James has a Growlithe back at home where he can use the stone to evolve it into an Arcanine. Not only that but they are ordered to not pursue in any more Pokemon hunting for the time being. They are dismissed with a large raise and smiles on their faces. 

It is then that Domino is called in to witness Mewtwo being released from the Master Ball. Giovanni pushes the button to release Mewtwo, pure energy comes out of the ball then materializes as Mewtwo. Giovanni welcomes Mewtwo home, only to see that Mewtwo is summoning an Energy Ball from its hands with intent to kill. Turns out while Mewtwo was captured, he does not obey Giovanni. Just as Mewtwo is about to go in for the kill, he collapses in agony. Giovanni has a device that sends a noise that causes him pain. Domino then starts beating up Mewtwo and puts a clamp on the tube structure behind Mewtwo ’s head. Mewtwo can't use any of its powers with this clamp on his external nerve cord. Mewtwo is powerless to do anything. 

A few weeks go by and Mewtwo is chained to a wall in a padded room where he is starving and beaten. The clamp is still attached to his nerve cord. It is here that Mewtwo is visited by the ghost of Amber. She is there to comfort him and gives him an idea. She tells Mewtwo to act broken and obey Giovanni for the time and only when his guard down can he gets his revenge. She also tells him that Lexi, Duke, and Erica are alive and locked up the Saffron State Penitentiary and he can still save them if he does this right. Amber then leaves as Giovanni enters the room and tells him that this whole mess was his fault. He could visit Amber as often as he wanted to had he just gone with Giovanni and no one would have died. Mewtwo breaks down and pleads Giovanni to set him free and is willing to serve him. Giovanni seems convinced that Mewtwo is finally broken and releases him and removes the clamp. 

Giovanni escorts Mewtwo to the training room where there is a set of power armor and suits him up. Giovanni turns the armor and Mewtwo realizes he can't control his body anymore. Giovanni puts on a special suit which allows him to control Mewtwo ’s body and informs the powerless Pokemon that Giovanni wasn't convinced that Mewtwo was truly broken. Now Mewtwo is Giovanni’s puppet which he will use to eliminate the other teams. Henceforth, Mewtwo is called Champion and he tries to step out of line, Giovanni will have Lexi, Erica, and Duke executed for being rogue Pokemon. End of part 4.

Part 5 begins in Saffron State Penitentiary where Erica wakes up in her prison cell. She is wearing an orange jumpsuit with the numbers 428, matching her Pokédex entry and her fur is completely shaved off. Even the areas of her large ears which now look much shorter without her beautiful fur. As she looks around trying to make sense of where and how she got here, she sees an infernape covering herself with a heated blanket and her flame is completely out. It is Lexi, and without her flame on her head, she is slowly freezing to death. Duke is nowhere to be found. 

The two of them try to comfort one another, Lexi says Mewtwo would never abandon them and will soon be here to free them, then Erica gives Lexi the bad news, Mewtwo has been captured and is not coming for them. Lexi breaks down in tears and claims all this is her fault. She regrets ever agreeing to aid Mewtwo. Just then, a cell door opens and two Pokémon are escorted by guards to their cells next to Lexi and Erica. These Pokémon are a female Zoroark named Hannah and another Pokémon that none of them are familiar with. A male cat-like electric type called a Zeraora, which was never given a name. The four Pokémon introduce themselves:

The story of Erica and Duke. (Part 5 goes into these Pokémon’s backstory)

Ten years ago, the Pokémon that would eventually become Erica was just a baby Buneary living in Eterna Forest with her family of wild Lopunny and Buneary. They were soon attacked by a pack of wild Houndoom. The parents tried to fend them off but are no match for these hounds. Erica flees her attackers and cries out for help as she is being pursued. Not too far away, Zackery Patrick is having a picnic with his Pokémon as they celebrate defeating the gym leader from Eterna City. That is when one of his Pokémon, Duke the Machop, hears a Buneary in distress. Duke leaves Zackery to see what the sound is. Zackery and the rest of his Pokémon follow behind. 

Erica is cornered with no way out as the Houndoom close in for the kill. Erica covers her eyes and cries out for help, that is when Duke jump kicks one of the hounds and protects Erica. Soon after, Victor the Riolu, Nathan the Chimchar, Caila the Raltz, and Gloria the Shinx, all join in the aid Erica. Zackery calls out to his Pokémon to drive the Houndoom back. 

After a fierce battle, the Houndoom flee, one of them is out cold, Zackery’s Pokémon are victorious and Erica is saved. Zackery begins looking around the forest for Erica’s family, only to find that the Houndoom pack are devouring what’s left of them. Erica’s family died protecting her and giving her a chance to escape. Zackery offers Erica to join him and his Pokémon and become part of his family. Erica willingly enters into a pokeball and becomes part of Zackery’s team and family. Zackery gives Erica her name based on a girl he had a crush on back in grade school.

As Erica stayed with Zackery, her feelings toward Duke grew stronger. After all, it was Duke that came to her aid and the two of them grew fond of each other. But one battle would prove to be too much for Zackery’s Pokemon, for Erica had not evolved into a Lopunny the same time as the rest of her new family and Zackery became concerned. All of his other Pokémon evolved just fine but not her. And when Zackery ‘s team was nearly defeated, Erica was his only option, but she was not ready. Zackery was up against a tough trainer and his Pokémon were all dark type, one of which was a Houndoom. Zackery sent in Erica to fight when he no choice. Duke and the others were defeated during this fight. And the moment Erica saw her opponent, she freaks out and hid behind Zackery and openly refused to fight. The judge was about to declare forfeit when Duke ( now a Machoke) gave Erica the best hug he could and told her everything was going to be okay and that he loved her. Hearing those words from her hero filled her with so much joy, she began to evolve right then and there into a Lopunny. 

With her newfound confidence and strength, Erica made short work of the Houndoom and the rest of the dark trainer’s Pokémon. She had overcome her fears and she had won. After the battle, Zackery used the prize money he had won to give his Pokémon a victory feast. They earned it. Caila and Victor ( now a Gardivour and a Lucario) told Zackery that Erica evolved out of love for Duke. Caila and Victor learned how to speak like humans and told Zackery how the others are feeling. They also told Zackery that Erica would rather be in beauty contests and Pokémon centers and not on the battlefield. After seeing the effort she put into saving the team from defeat, Zackery agreed that Erica would be the beauty queen of the team. And he chose wisely, as Erica would win beauty contest after beauty contest for eight years straight. 

After those eight years, something happened that no one saw coming, Zackery retired from Pokémon training. Not only did Erica win so many awards and prize money, but the rest of his Pokémon were Sinnoh state champs and World Series champions during those eight years. It got to the point where Zackery could retire at age 20. And an even bigger shock is when he told his Pokémon that they could either stay or leave. Nathan, Victor, Caila, and Gloria all chose to stay. Duke wanted to leave, the only way he could reach is final form as a Machamp, was to either be traded to another trainer or leave. Erica didn’t want to leave but he didn’t want to leave Duke behind either. But she also knew that Duke wants to be stronger and that taking that chance away from him wasn’t loving him. With tears in her eyes, she gave Duke a goodbye kiss and sent him off. 

The next few months, Erica was in a deep depression, and nothing Zackery did could cheer her up. He began searching for any leads on Duke, and he found him. Zackery contacted him and asked to come back to be with Erica, he did the next best thing. Duke sent him front row tickets to his next fight. Erica was overwhelmed with joy, but there was a problem, Erica couldn’t speak like a human. Without this ability, a careless Pokémon trainer could mistake her for a wild, lost, or rogue Pokémon; neither of which were good for Erica and she would need to gain citizenship so she could get work. Erica was so used to being with humans that she wouldn’t do well in the wild. So for the next several months, Erica behaved and talked more like a human than a Pokémon. When she was ready to leave, she had a perfect understanding of human speech, basic math, and could read maps. And with that Erica left her family to be with the love of her life. 

She arrived at Canalave City where Duke is scheduled to fight a world-class fighter: Russell the Incinoroar. The stadium is packed with fans as this is a championship tournament with a live rock band called Like’n’Rock. The tournament was noisy, but that didn't stop Erica from being with her champion. Russell appeared first on the ring, then Duke. The two shook hands as the cage closed around, and the fight was on as the band played heavy metal music. At first, Duke was winning, but this was a false sense of security, Russell wins by wearing his opponents down then goes in for the final tackle when his opponent is tired. Russell goes in for a smackdown, but Duke isn't fooled. With a mighty seismic toss, Duke defeats Russell and becomes the new champion. Erica rushes to the ring hopping over the security guards and embracing her lover. 

Over the course of one year, Duke became the Pulverizer and Erica got a job working as a daycare assistant and the two of them were happy together. But one day, something terrible happened. Duke was up against a Medicham, and lost horribly to this Pokemon and lost his championship title. Duke had met his match and his career as a professional wrestler was over. And Erica was fired from her job at the daycare, her new boss didn't want a ”sexy Pokemon” near children out of fear that she might give children immoral thoughts of being with a Pokemon like her. 

The two of them searched for work, but all they could find was a bar job in Kanto which was under the management of Lexi the Infernape. She gladly hired these two, together they worked to keep the bar alive and well. A year later, Mewtwo arrived and changed their lives forever. 

Flash forward to the Pokemon in prison as Erica finishes her back story. Lexi is too tired and weak to tell her story. Hannah the Zoroark tells her story as to why she was here in prison. She had brutally murdered her abusive Pokemon trainer and was given an unfair trial. She has been sentenced to death and informs the Pokemon here that these cells they are in are for criminals on death row. They may have only one month to live. 

Zeraora is not on death row, for his cell is more of a scientific chamber than a normal cell. He claims he is only here until the humans can find a suitable lab so he can be studied. The cells in death row were the only ones large enough for him and his chamber. As far as he knows, he is the only one of his kind, and he was captured in the wild and brought here for the time being. Yet he can understand and talk to these Pokemon despite living in the wild all his life. After hearing their stories, he decides that humans are a blight upon the earth and will do what he can to punish them for their mistreatment of Pokemon. Erica argues that Zackery isn't evil, and therefore not all humans are to be punished for other’s actions. But Zeraora doesn't want to listen. The two of them argue for a while until Lexi shouts at them to shut up so she can sleep. As they rest, Lexi can't stop thinking about Mewtwo and how he is doing.

Jumpcut to Team Flare’s headquarters in Kalos being attacked by Mewtwo. He is wearing the armored power suit placed upon him by Giovanni and he is ruthlessly killing all Team Flare members one after the other. Not even the Pokemon working for Team Flare are save. Turns out Mewtwo has no control of his body or powers. Giovanni is wearing his own power suit and has full control of Mewtwo while wearing the suit. Mewtwo can watch in horror as he sees all these people and Pokemon due right in front of him, and there is nothing he can do. 

Turns out Giovanni is using Mewtwo as a weapon to wipe out the competition of top crime syndicates is every state and region in the known Pokemon world. There is a bloody and gruesome montage of other crime syndicates being destroyed by Mewtwo. Team Aqua, Team Magma, Team Galactic, and Team Plasma don't stand a chance. These teams use guns, and other Pokemon to fight back; all useless against Mewtwo. This goes on for a month, mere days before the Pokemon at death row are scheduled to die and Mewtwo has a mission in the Alolan Islands to hunt down and destroy the Aether Foundation. Giovanni isn't going to waste his time with Team Skull as they are nothing but worthless street thugs in his eyes. 

Mewtwo is transported there by helicopter just like all his other missions with Domino debriefing him about the mission. What Mewtwo finds is a clean lab in the middle of the ocean of the coast of these islands. At the center of the lab is an Ultra Beast in an isolation chamber. They don't know what an Ultra Brast is, but they will kill all members of the Aether Foundation just to see what it is the Foundation has captured and if it is worth anything to Team Rocket. 

Mewtwo finds a Type:Null guarding a human mother and her two children, Gladion and Lillie. Giovanni recognizes the woman as the founder of the Aether Foundation and commands Mewtwo to kill them. As Giovanni moves his body, he feels restricted in his motion suit. Mewtwo is resisting Giovanni’s command, which gives Gladion just enough time to activate a machine that creates portals into the Ultra Beast realm. Mewtwo is sucked into the portal and Gladion closes it. Mewtwo is trapped in the Ultra Beast realm, this causes Lexi to wake up from her freezing sleep with a sense of absence in her life. All she can do is wonder why she feels this way. 

Mewtwo gets up to discover a world he is not familiar with, and Pokemon no one has seen before. Mewtwo is ambushed by these powerful Pokemon lead by Necrozma. Mewtwo fights for his life and ultimately wins and demands a way out. Necrozma opens a portal back to the Aether Foundation where the others are just now making their escape. Mewtwo passes out on the ground from his battle with the Ultra Beasts and his armor needs serious repairs, Domino puts Mewtwo back in the master ball and heads back to the helicopter. Gladion and his family with Type:Null make their escape on a boat as they watch the Foundation headquarters go up in flames by Team Rocket. Lexi then feels relieved but she can't explain why. She goes back to sleep feeling a little warmer.

Mewtwo wakes up on a medical bed with a rebreather on his face and bandages of over his body, he is a mess. With him are Giovanni and Domino as they tend to his wounds. Giovanni orders Domino to leave so the two of them can be alone. Domino closes the door behind her. Giovanni is furious that Mewtwo let key members of the Aether Foundation escape and no rare Pokemon were captured. Mewtwo explains that his suit malfunctioned and that is why he failed. Giovanni buys into his lie and promises Mewtwo a new set of armor and his word that if Mewtwo success in one last mission, he will get his friends out of prison and drop all charges on them. 

The next day Mewtwo slips into his new armor and is plugged into a charging station, give him and his new suit a stronger charge of power and energy. He is left alone as the machine does its thing. To Mewtwo ’s surprise, he can sense the world around him. He tries to contact his friends using his newfound power. To his shock, he feels a great deal of pain, as if he was fighting the Ultra Beasts again. But this was not his pain he was feeling, it was Lexi’s. Because her flame was burnt out for a long time; her strength, her will, and reason to keep living were burnt out as well. Meaning that when Team Rocket disguised as guards would go into her cell to so evil abominations to her, she could defend herself no matter how hard she tried to fight back, she was just too weak. None of the other Pokemon could help her either, they each had their own cell that they couldn't escape from. But Lexi has been so badly broken by physical abuse that she wanted to die rather than go through another beating. This crushed Mewtwo’s heart to the point where he decided that today was the day he would finally get back at Team Rocket. Enough is enough. 

Mewtwo is given instruction from Giovanni to try out his new suit on an unsuspecting Pokemon trainer who has agreed to take on the ultimate gym challenge. To Mewtwo’s surprise, it is Ash Ketchem with Pikachu, Misty, Tokapi, and Brock. Giovanni activates the suit and Mewtwo has lost control of his body once again. But before Mewtwo is completely helpless, he sends a quick Psychic message to Pikachu begging to attack him with a thunderbolt as quickly as possible. Pikachu does just that and hits Mewtwo with a thunderbolt so hard, the gym goes dark and all electronics go down. After Mewtwo thanks Pikachu for freeing him, he goes wild and begins to destroy the building. Giovanni activates the device that sends a noise to Mewtwo so painfully high pitched that Mewtwo collapses and cries in pain. Just then, Domino comes into the gym floor to retrieve Mewtwo. Despite the pain, Mewtwo ignores it long enough to shatter the master ball with his mind and shred Domino with the pieces. Mewtwo can't take it anymore and grabs Ash and Friends and teleports out of the gym. Stunned by what just happened, Giovanni regains his train of thought and orders Team Rocket to find Mewtwo and to clean up the mess. End of Part 5.

Part 6 takes place on Cinnabar Island when Mewtwo teleports onto the Island. With him are Ash, Misty, Brock, Tokapi, and Pikachu. They are afraid to approach Mewtwo as they just saw him wreck the Viridian City Gym and took them to an island in an instant. But Mewtwo isn't attacking them, in fact, he isn't moving at all. Mewtwo begs Ash and Crew to help him get the armor off him as it is weighing him down and he used all his energy to teleport them out of the gym. Pikachu and Tokapi go to help Mewtwo despite their owner’s demands. Then Brock goes to help and removes Mewtwo’s helmet and sees a broken Pokemon bleeding at the ears. Ash and Misty join in and help take the armor off piece by piece. But one piece is burnt onto Mewtwo second neck, a computer chip that was fried when Pikachu hit Mewtwo with a thunderbolt. Brock carefully cuts around the chip and removes it without damaging Mewtwo ’s nerve cord. Mewtwo simply rests against the sands of the beach as Brock applies heal sprays on his wounds. Ash and Misty ask Mewtwo why he was there at the gym. Mewtwo catches them up on all the events that have happened in the past month and a half. 

Brock finishes healing Mewtwo and suggests that Mewtwo rests to fully recover. But Mewtwo realizes that his friends are still in prison and he needs to free them soon. He tells Ash and friends to not report him to the police anything for they work for Team Rocket. He teleports them to Pallet Town then flies over to Lavender Town. He needs a ghost type Pokemon to go through walls undetected and find his friends, he is hoping at least one of them will cooperate.

Meanwhile: Jesse, James, and Meowth are staring death in the face as Giovanni is fuming in his office. Giovanni asks if that Pikachu that landed that hit on Mewtwo was the same Pikachu that they were trying to steal for him all this time. They answer him honestly and are given a new assignment: Find Mewtwo, recapture him. Find Pikachu, kill him, and his trainer. If they do this, they will finally be elite members of Team Rocket.

Later that night in Lavender Town, Mewtwo enters the cemetery tower where all dead Pokemon are buried by their trainers to be laid to rest. He calls out to the ghost Pokemon hiding in the shadows to come out. A Gengar reveals himself to Mewtwo with a sinister grin on his face. A Haunter and Gastly try to attack from behind but Mewtwo dodges their attacks. Just as things get heated, a familiar voice stops them all. Simon the Chandelure, this time with a different color palette, reveals himself and Mewtwo couldn't be happier to see him. Simon, is angry at Mewtwo. He had died a second death and is still trapped in this world as a ghost type with no way of knowing how to move on. He blames Mewtwo for the month and a half that he had to endure alone and is just back where he started. Mewtwo explains that the others are still alive and need their help. Simon agrees to help, but only if Mewtwo leaves afterward and never returns. Mewtwo agrees that their lives are worse now than ever before and promises to leave them be. The two fly off toward Saffron State Penitentiary 

Mewtwo and Simon hide just outside the prison walls. Simon will find their friends and Mewtwo will cause a distraction so Simon can use his fire abilities to get the others free. Simon sneaks his way through the prison, phasing in and out of walls as needs be and he finds Duke in a steel coffin but still alive. Simon melts the locks and sees that Duke has lost his power belt and his muscle mass. Duke is a walking skeleton at this point. Simon tells Duke to stay put while he goes looking for the others. He finds Erica and Lexi and is overjoyed to see them again. Erica gives him the biggest hug and tells Simon that Lexi’s flame is out. But the smoke detectors goes off and the prison goes into lockdown. Mewtwo sticks to the plan and attacks the prison outer walls causing them to crumble all around the prison. Simon gives Lexi his flame and she instantly gets her strength and power back, and she is livid. She uses her flame to melt the steel bars of her cell, them does the same for Erica. Guards swarm in to stop the escaping Pokemon, but Lexi grabs a steel bar and beats the guards to death with them. 

Mewtwo sees a padlock in the prison and uses his psychic powers to unlock all prison doors and start causing a full prison riot. This means Duke, Hannah, and Zeraora now have a chance to escape. Duke makes a run for the storage rooms to find his belt. Simon leads the others to the same location to get all their personal belongings back. It is in that same room where Erica and Duke are back together. Simon finds Duke’s belt and Duke is back to the way he was at full power. Lexi sees one of the guards who abused her and goes in for the kill. She tackles him to the floor and pins him down. She then incinerates her abuser right in front of everyone without the slightest care. It is clear that Lexi is just broken, but Mewtwo breaks the wall next to them and all are relieved to see him, Lexi gives him a death glare. Mewtwo instructs the Pokemon to grab his tail if they want to leave. Simon, Erica, Duke, Lexi, Hannah, and Zeraora do so and Mewtwo teleports out of there with his friends just as the police arrive. 

Mewtwo and friends arrive at the most isolated islands in the Orange Archipelago and Mewtwo says they will be safe here. Lexi beats up Mewtwo with a steel rod and pins him down. Lexi demands what Mewtwo has been doing this whole time. Mewtwo explains that he too was a prisoner and he felt all of Lexi’s pains because he put a psychic link on them just he loves them, especially Lexi. She then breaks down in tears and Mewtwo hugs her right so she will have a shoulder to cry on. Simon can't bring himself to separate the two of them and tells Mewtwo he can stay. Erica notices that Simon is fading. He is finally moving on to the afterlife. Everyone says tearful goodbyes before Simon fades completely. Mewtwo promises to never leave his family ever again or to put them in any kind of danger. Hannah and Zeraora decide to stay with Mewtwo.

The next day, the governor of Kanto issues a state of emergency, placing Mewtwo and all Pokemon that escaped with him as S Rank Rogues and are to reported or killed on site. News of the prison attack spreads across the world as well as an international bounty on the Pokemon. Beth learns of the attacks and tries to defend Mewtwo as a hero and used her son, Tommy as proof of her testimony. Others like Gladion condemn Mewtwo as a monster who needs to be put down. The world is falling into chaos.

Elsewhere, in the state of Sinnoh, a young man name Zackery Patrick is caring for the Pokemon at a local nursery. He then returns home where he has six Pokemon of his own who still live with him and also have jobs. It seems being a Pokemon champion right years in a row can only get one so far. His Pokemon are Nathan the Infernape, Caila the Gardivour, Gloria the Luxray( who can't speak), Justin the Floatzel ( can't talk), Alexander the Staraptor (can't talk), and the strongest one of them all; Victor the Lucario. Zachary returns home to find his Pokemon glued to the TV screen. The news of Mewtwo’s attacks has reached Sinnoh and they make the shocking discovery that Erica and Duke are in on the attacks. Zachary and his Pokemon agree to stop Mewtwo and get Erica and Duke back. The Pokemon go into their Pokeballs except for Alexander, he is going to fly Zachary to Kanto. Zachary stops by a store first to pick up a special device. 

Alexander flies to Mt Moon in Kanto and land nears the summit. Zachary dismounts and puts Alexander back into his pokeball so he doesn't freeze to death. The summit is cold even in the hottest summers, but this peak overlooks all of Kanto. Zachary lets Victor out and is told to find the missing Pokemon from this elevation. Victor has the ability to pick up the aura of all lifeforms within a 100-mile radius. All he has to do is meditate and he can find them. After thirty minutes of concentrating, he finds Erica’s aura far to the south. Zachary releases Alexander and they both mount the massive bird and head south, toward the Orange Islands. End of part 6.

Part 7 opens with a log cabin deep in a jungle. Mewtwo opens the door from the inside to get some fresh air. Ahead of his is a path that leads to a beach. On that beach, he sees Hannah and Zeraora training for battle. To Mewtwo’s right, a clearing in the jungle where Duke is chopping logs in half with his bare hands and Erica napping on a hammock. Behind the cabin is a hot spring where Lexi is lounging in the pools of scalding hot water. Mewtwo goes to be with her, keeping his promise not to be without her. Mewtwo and Lexi are a couple now, and they are deeply in love with one another. So much so that they decide to go inside for a little alone time. 

Erica wakes up from her nap and goes for a walk in the jungle. As she wonders she finds a new beach and there are no islands anywhere in sight. She hears a Staraptor, at first, she thinks nothing of it, until she realizes that these Pokemon are not native to this area. She looks up to see the Staraptor pass overhead and see a Lucario fall from the sky toward her. He lands feet first in the sand, then slowly rises, staring down Erica with a look of starting trouble. The Staraptor comes back and lands on the beach behind Erica. Zachary dismounts and slowly walks toward Erica. She isn't sure if she should be happy to see her former Pokemon trainer or should be very concerned. Zachary tells her that he is here to take her and Duke home and turn in the others for the high bounty on their heads, especially Mewtwo. Erica tries to reason with Zachary, but he is not in a listening mood. He lets the other Pokemon out of their balls and tells Erica that she can come home or go back to prison, but Mewtwo was going to pay for his crimes one way or another. Just then Victor rushes in to guard Zachary because Mewtwo and the others showed up. Mewtwo also tries to reason with Zachary but again he is not listening. Caila warns Mewtwo that any mind-reading will be met with resistance. It was then that Victor proposed that a battle is settled this argument and Mewtwo agrees. Erica warns Mewtwo that Victor is the world’s most powerful Lucario and psychic types like him are nothing to Victor. Mewtwo claims that Victor has never faced him and that he is much stronger now than ever before. 

Mewtwo and Victor are getting ready for the fight of their lives. Victor goes in for the attack and Mewtwo simply dodges each and every attack. Then when Victor starts to show fatigue, Mewtwo goes in for a series of attacks to the point where Victor is badly wounded. But Victor refuses to stand down. So Mewtwo beats up Victor again. Victor tries to get up refusing to surrender, but Mewtwo hits Victor so hard that he collapsed and is knocked back to Zachary. Victor can't get up and he failed to land a single hit on Mewtwo, at this point, Mewtwo is mocking Zachary and his Pokemon. Caila decides to fight Mewtwo next while Zachary heals Victor. As the two Pokemon take their battle to the sky, Zachary ’s Pokemon guard him while he heals Victor of his wounds. Lexi tells the others to not worry about it, Mewtwo has this under control. 

Neither Caila nor Mewtwo can land a single on each other. But the battle becomes loud that all residents of the Orange Islands can hear it. Even Jesse, James, and Meowth of Team Rocket. They steal a boat from a Marina and headed to the battle. With them are Greninja, Blaziken, and the other Pokemon who are seeking revenge from being defeated by Mewtwo before. They speed across the sea toward the island and can see battle in the sky. They are too far away to join in the fight, but they are closing in.

Zachary finishes healing Victor who is livid and ready to get back in the fight. Mewtwo finally lands a hard hit on Caila and sends her to the ground. Caila is down and Victor wants to get out there and fight. Zachary activates the special device, it is a mega stone activator and it transformed Victor into a Mega Lucario. With this new form, Victor was much faster and stronger than Mewtwo. This time, Mewtwo was outmatched and was beaten up. Afterward, Victor grabs Mewtwo and gives him a crushing hug directly on his chest spike, leaving a near-fatal wound on Mewtwo chest just before being thrown into the sea. Zachary is angry at Victor for basically killing Mewtwo, they needed him alive for the bounty. But Victor has a change of personality and is very hostile toward everyone. Caila wakes up and sees Victor as a monster. Zachary rushes over to use the last of his supplies to heal Caila, he then tries to return Victor to his ball, but it got damaged during the battle. Lexi steps forth to challenge Victor, she just watched the love of her life get beaten to death and drown in the sea. She is going to kill Victor and she wastes no time going in for the attack. She lands hit after hit put Victor treats these attacks like they are nothing. Lexi gets hit once and is sent flying through trees in the jungle. Erica, Duke, Hannah, Zeroaro, Nathan, Gloria, and Alexander all join in to stop Victor. Justin goes into the sea and tries to find Mewtwo at the bottom of the sea. Lexi comes raging out of the jungle and gets back in the fight.

At the bottom of the sea, a lifeless Mewtwo slowly drowns in the water. He hears a voice call out to him, he opens his eyes to see Amber looking at him with disappointment. Amber orders him to get up and fight, this battle isn't over. He feels Lexi's life force go out and that is when he charges up all his energy and flies up out of the water. He hovers above the sea holding Justin in one hand and is fully healed. Across the beach are beaten and wounded Pokemon and Victor standing on the beach waiting for a rematch. Seeing this, Mewtwo taps into a new power he never unleashed before. This new power allowed him to transform him into Mega Mewtwo X. Now Mewtwo and Victor are an even match and their fight is so intense that the weather changes into a storm. Caila does her best to use her healing power to revive all fallen Pokemon as the others take cover behind boulders. Amber is with Mewtwo giving him orders on how to defeat Victor. 

Amber orders Mewtwo to hit Victor with a powerful sky uppercut, he does so and it Victor so hard that his mega form gets knocked in pieces and sends Victor in his base form skyward. Mewtwo then flies up and slams Victor down to earth. Just before Victor hits the ground, Mewtwo teleports to the ground and kicks him so hard that it sends him into a rock wall. Victor hits this wall so hard that it causes the mountain to explode, chunks of the mountain fall into the sea. A stunned Team Rocket then turn around, they realize that Mewtwo is far too powerful to take on themselves. 

Victor peels of the rock wall and falls dead on the sand. Mewtwo then transforms back to his base form and kneels on the sand to catch his breath. Lexi rushes over to Mewtwo to check on him. Zachary rushes over to Victor just as the weather changes back to normal. Zachary goes through his bag and finds no revive potions or heal potions. Caila flies over to use her healing powers, but she can't. She had used all her energy healing the others. Zachary and Caila start crying over the loss of Victor. Mewtwo walks over to Zachary and says that he can save Victor but only if they leave the island and never return. Zachary agrees, Mewtwo grabs a teardrop from Caila and places it on Victor. Mewtwo uses his power to fully heal and revive Victor. He wakes up and Caila gives him a big hug. Mewtwo tell Zachary to take his Pokemon back to Sinnoh and take the other Pokemon back as well. Lexi refuses to leave Mewtwo, but the others all decided to go with Zachary. Luckily, Zachary did bring enough spare pokeballs that they could all be taken to Sinnoh. Mewtwo and Lexi go back to the cabin while Zachary takes all other Pokemon back to his home. 

That night, Lexi wakes up to find Mewtwo missing. She looks around for him and finds him meditating on the beach. Lexi checks upon him, he wakes up and tells Lexi that he has a plan to end Team Rocket once and for all. He is simply going to destroy all structures that house them inside and kill all members on site. If the state of Kanto has condemned him and his friends as rogues, then he is going to destroy everyone who destroyed his life and not give the slightest care for the law. Mewtwo knows that he just brings the worst of humanity out and he must end it all. Lexi is concerned that Mewtwo might have become savage like and warns him that the kind of behavior he has could lead him to his death. She doesn't want to say goodbye to someone she loves again. The two of them head back to the cabin to get some sleep. End of part 7.

Part 8 begins onboard a helicopter where Giovanni is riding on his way the same island where Mewtwo was made. He, Butch, and Cassidy leave the copter and enter the lab. The scientists there are nervous about Giovanni’s arrival, they are trying to create another Mewtwo but are creating nothing but Dittos. Giovanni is here to offer some blood to use the complete the genetic code to create a proper Mewtwo. As soon as Giovanni leaves, he receives a call from the scientists that his blood is mixing well with the DNA samples they have and a proper fetus is in the making. This is good news for Giovanni, soon he will have a Mewtwo that is loyal to him. But he still needs to find his former champion and put him down. 

It has been one week since Mewtwo fought Victor, he and Lexi are the only ones on the island and the days are too quiet. Mewtwo and Lexi hardly speak to each other and they are becoming more distant. Mewtwo just wants to be left alone but Lexi is worried for him. She tries to keep their love going but nothing is working, it finally reaches its breaking point. Lexi has had enough of Mewtwo keep his distance and demands answers. Mewtwo wants to leave the island and finish off Team Rocket once and for all. Lexi demands that he stays and not bother the humans. If he goes back to Kanto, ever Pokemon trainer and law enforcement officer will hunt him down. For Mewtwo, the hunting and hurting stop once everyone who spread lies about him dies and he gets Lexi her life and freedom back. Lexi claims her life is with Mewtwo and that there is no life outside of him. But no loving words seem to be working on him. Finally, Mewtwo asks Lexi a very personal question. If she was in his place, what would she do if evil people killed Emily? Lexi begins to choke up and tells Mewtwo that wasn't fair. Lexi has never spoken about Emily to anyone, not even to Erica and Duke. Lexi gets very defensive but finally breaks and tells Mewtwo why Emily is so personal to her. 

(Lexi’s backstory)

Before she was Lexi the Infernape, she was just a baby Chimchar and was given to a spoiled rich girl named Megan. Megan had no love for her Pokemon and had no desire to properly train them for battle. As a result, Lexi would lose fight after fight. Finally, it got to the point where Lexi was left abandoned by Megan. Lexi his under a park bench to get out of the rain and wept all day. That night, it rained hard and the flame on her tail was going out until a Popplio named Maria came over and covered her from the downpour. At first, Lexi was scared but calmed down and her flame grew bright. Maria led her out of the park bench and that is when she met her, Emily. She was a Pokemon trainer who took care of her Pokemon and properly trained them to be their best. Emily offered the frightened Lexi some Alolan Beans, one bite and the two of them became friends. 

Emily took her to the nearest Pokemon Center to be treated for any illnesses or injuries. Once she was healed, the nurse told Emily that the Chimchar already has an owner, and as it turned out, Megan arrived to get her Pokemon treated. Emily and Megan know each other as enemies, Emily kept Lexi a good save distance from her. Megan left and told Emily she could keep that weakling for all she cared. Lexi became Emily’s main Pokemon from that day forward. Lexi received her name that same day too, the name coming from Emily’s little sister back home. 

Emily's main team was Lexi the Infernape, Maria the Primarina, King and Queen the Nidoking and Nidoqueen, Rachel the Vespiquen, and Larry the Dragonite. She loved her Pokemon and they loved her back; together they won battle after battle, earn gym badges on after another. On their journey to the championship games, TM Talk was just announced in which Pokemon could learn how to speak like humans. Lexi wants to learn this move so she can thank her trainer properly. Emily used this TM on all her Pokemon so now there is a perfect communication between Pokemon and trainer. 

They made it to the Alolan State Championship and are victorious all the way to the final match. Emily's next and final opponent is Megan with her team of powerful Pokemon. They are Arbok, Snorlax, Raticate, Empoleon, Jolteon, Salazzle. During the battle, each trainer gained five victories and five defeats. The last round was Lexi verses Snorlax. But this Snorlax was much larger than most of his kind and has been known to crush his opponents with one body slam. And that just what Megan’s Snorlax does, goes in for a crushing blow. But to everyone’s astonishment, Lexi let Snorlax land on her. But she isn't crushed, she is holding the Snorlax with a stiff arm, breaking the Snorlax’s back paralyzing it. Lexi wins the match with one move and the crowd cheers her name. Emily and her Pokemon won the championship title. Megan is furious and storms out of the match. She can't believe that Lexi defeated her Snorlax with one move, her hatred toward Lexi is complete and she is going to ruin her. 

A few days later, Emily has her bags packed and is ready to go home to Kalos. She and Lexi are on their way toward the airport when they are ambushed by Team Skull. Lexi guards Emily, but one member shoots his gun and lands a shot at Emily, killing her instantly. Before Team Skull can get another shot, Lexi uses a flame wheel to kill all but one member of Team Skull. She gets the last member to talk by brutal force and it turns out Megan hired them to kill her and Emily for her defeat at the Pokemon Tournament. Lexi kills him after the is given the information then rushes Emily to the nearest hospital. There is nothing the doctors can do, she’s gone. Lexi tells the local police what happened and she is not charged with murder, her case was an act of self-defense. Megan is soon found at the airport and is arrested, her Pokemon are confiscated and she will be spending life behind bars. The police use psychic type Pokemon to confirm that Lexi was telling the truth and Megan really did hire Team Skull to act her revenge. The Alolan Pokemon League then changed from traditional gym battles to island trials because of the incident. Emily’s Pokemon are all set free or given to her family back in Kalos. Lexi went to the coast the let Maria out of her Pokeball one last time, she told her everything and the two of them parted ways. Maria went to the sea to live a free life, Lexi went to find work. She heard there were jobs open in Ryme City for Pokemon like her. She found one at a steel forge, she took it. 

Lexi worked at the forge for three years before it was shut down due to financial reasons. She got on a train to Kanto to find work and that is where she met Simon. He was sleeping on the streets and had one too many drinks. He wakes up to see Lexi and asks for spare change. Lexi used all her cash for her train ticket and food she bought at a fast-food restaurant, she instead offered him some of her meal. She felt pity for this Pokemon and told him the job she was going to was looking for help. Simon agreed to join her and the two of them became friends. 

One year later, they were both fired after Simon got so drunk, he burned down the restaurant they worked at and the apartment they stayed in. Lexi had to use Emily's winning money to pay for damages and had to find work in Fuschia City. Simon begged Lexi not to kick him out and he will make it up to Lexi. She kept him on a short leash and they found work at a bar; two weeks later, Erica and Duke were hired. To this day, Lexi always gets a hair cut that mimics Emily’s hairstyle; right side short, left sidelong.

After she finished her story, Lexi now understands why Mewtwo is so fixed on finishing Team Rocket off; he needs closure. The same closure Lexi got when Megan was finally brought to justice. With tear-filled eyes, she told Mewtwo he could go, fearing that he may never come back. Mewtwo gave her a sincere hug, teleported them both to Zachary ’s house, and left for Kanto. Lexi will be safe and with the company while Mewtwo acts his revenge. End of part 8.

Part 9 starts with a news report that Mewtwo is back and is attacking cities all over Kanto. The state is on high alert and not even the military can stop him. Yet Mewtwo is sparring the lives of soldiers, citizens, and Pokemon alike. One survivor says he was saved because he wasn't Team Rocket. Watching the news is Xavier the Alakazam in his apartment. He was the Pokemon who was assigned to track down Mewtwo, but he was secretly working on his own project; finding out who Team Rocket is and why would a Pokemon go through all this trouble to hunt down an urban legend. On his wall are newspaper clippings of all of Mewtwo ’s activities and missing children cases. He is trying to see how they are all connected. 

Xavier hears an explosion in the distance, he knows Mewtwo is here. Xavier was about to leave his apartment but is stopped by Mewtwo. Xavier is completely powerless compared to Mewtwo and is at his mercy. Mewtwo just wants to talk and give Xavier all the evidence he needs to clear his name of all crimes. Mewtwo then rearranges all of Xavier ’s newspaper clippings and reveals that Giovanni of Viridian City is the real criminal and Mewtwo is just one of his countless victims. Mewtwo then leaves a flash drive with Xavier, it contains all of Team Rockets locations, money transfers, and lists of names of children and Pokemon kidnapped by them. Xavier will do what he can to get Mewtwo’s name cleared. He then leaves for Viridian City.

Elsewhere, the legendary Lugia flies over to Kanto to meet an old friend. She can feel the fear of thousands of worried souls and decides to investigate. She arrives at the World Tree near the base of Mt. Moon where she meets Mew. Mew has been the guardian of the Tree for centuries but behaves like a child compared to Lugia. Mew has a collection of toys that he’s gathered over the years to keep him entertained. Lugia asks if he noticed any strange activities in Kanto. Mew says that he tends to not interfere with humans and has not noticed anything strange. 

Mewtwo arrives at Viridian City high above the city skyline, Giovanni and Team Rocket are trying to make their escape by helicopter but Mewtwo destroys it from a distance. Giovanni tries to the sonic device that crippled Mewtwo before, but the Pokemon is too far away for the device to have any effect. Mewtwo creates an energy ball that he will use to destroy the Viridian City Gym and everyone inside. The ball grows bigger as Team Rocket hides back inside the building. 

Lugia and Mew see a massive energy ball being created in the far distance. Mew decides to go stop whatever is causing it, Lugia wants to join in, but Mew reminds her that she can't transform to hide in plain sight and the Tree always needs a guardian. Mew then transforms into a Pigdeot and flies toward Viridian City. 

Mewtwo throws his ball of death toward the gym and it hits with a force of a nuclear bomb. The shockwave heads straight for Viridian City, but Mewtwo stops the wave using his psychic powers, saving the city. All the remains of the gym are rubble and a bombproof shelter. Mewtwo rips the door down and orders everyone inside to come out. It is Giovanni, Jesse, James, and Meowth. The rest were vaporized in the blast. 

Just as Mewtwo is about to get his revenge, Mew kicks him in the jaw, knocking him away from his targets. Everyone is in shock to see a Mew in person, most people believed that Mew went extinct a millennia ago. Mew tells Mewtwo that there has been enough killing today and he needs to stop. Mewtwo is not listening and orders Mew to move aside or go extinct. Mew teleports behind Mewtwo, wraps his tail around Mewtwo’s second neck, paralyzing him. Then Mew throws the Pokemon so hard he crashes into a mountain and stops inside Cerulean Cave. Mewtwo is out cold as he floats on a lake in the cave.  
Mew then checks on Team Rocket and tells them he can take them to any safe place. Giovanni demands that they need to go to the research island. Mew does just that. Before Mew leaves to go check on Mewtwo, Meowth gives his a hero a goodbye hug, them Mew leaves. Giovanni realizes that Meowth has some Mew’s hair on his body and is taken back to the laboratory. On the horizon, boats approach from the west. They are members of Team Rocket from the Johto region coming to help the boss. Giovanni feels that things are finally working out.

Mewtwo wakes up in the middle of a lake deep in Cerulean Cave. He heals himself and is overcome by pure rage. Mewtwo snaps and explodes in a violent first, sending a shockwave so powerful that it destroys the cave and half of the mountain. Mewtwo finds Mew and the two Pokemon get into an epic fight. At first, Mewtwo has the upper hand, but Mew then transforms into his opponent and now it is a fight of titanic proportions. It is a fight so intense that it could be heard from all parts of the world. The earth shakes, waves become tsunamis, winds become hurricanes and the world is in panic. Mew launches a massive energy ball at Mewtwo and he does the same at Mew. The two energy balls clash and exploded with a force of a thousand nukes. Leaving a massive crater in the desert where they fought. Despite the damage both Pokemon are alive, but mortally wounded. Mewtwo limps over to a broken Mew and gently grabs him and tucks him in his good arm. Mewtwo uses the last of his energy to teleports him to Pallet Town, in Mewtwo ’s old bedroom in Samuel Oak’s lab. He bursts into the room soon after with a shotgun but doesn't pull the trigger once he realizes who it is. 

Mew is placed into a healing tank while Mewtwo lays in his bed being treated for injuries. He tells professor Oak everything. He believes the wounded Pokemon and will back him up in any way he can. Ash and his friends told him the same story two weeks and are staying in Pallet Town until things calm down. The news is flooded with reports about Mewtwo, but on of them has a report by Officer Jenny and Xavier saying that Team Rocket are very real are Mewtwo is just hunting them down and being brought to justice. They say that all information about Team Rocket is being made public and if you find any members of Team Rocket including Giovanni, report them to the police at once. All crooked cops have already been arrested. Mewtwo can rest easy knowing that his name has been cleared. 

On the research island, Giovanni hears over the radio that his cover is blown. Police forces all over the world are now a manhunt for him and Team Rocket. Butch comes to tell the boss something has happened to the new Mewtwo. They return to see that this Mewtwo in the lab is full grown, black with a grey tail and has an orange crystal growing out of its left shoulder. The scientists explained that it spontaneously grew into this the moment the Mew hairs were added. Giovanni has a sinister grin on his face, he wants to talk to this dark Mewtwo at once. That is when it woke up and sees Giovanni for the first time. The two of them have a personal talk via telepathy. The two of them talk about world domination and the destruction of Mewtwo. Giovanni gives this dark Mewtwo and nickname: Shadow Mewtwo. Giovanni, then asks if it was possible to find Mewtwo using telepathy. Shadow Mewtwo goes back to sleep and tries to locate this other Mewtwo by the mind.

That night, Mew and Mewtwo are sleeping, they share the same dream together. But this is no dream, this is a mind link. Mew is in a limbo of white with Mewtwo. There are two portals with them; one leads to Mew’s thoughts, the other leads to Mewtwo’s thoughts. Mewtwo leads Mew into his portal and Mew sees what has happened to Mewtwo in the past until now. Mew now understands that Mewtwo isn't evil, but Mew is still opposed to simply killing those who did wrong. Just as Mewtwo is about to justify his actions, the portals close and the endless void of white turns black. There is another Mewtwo with them with the piercing orange area around it and it demands that Mewtwo return to the island where it all started. Then the dark Mewtwo leaves the dream. Mew and Mewtwo realize that there is another Mewtwo out there and if it fell into the wrong hands, it could mean the end of the world. When Mew asks what island it was referring to, Mewtwo knows it as the island research center where he was created. He then asks Mew if he had and Pokemon he could recruit to aid in the expected assault. Mew says he knows a few friends that could help out. Mewtwo will head to Sinnoh to get his Pokemon and Zachary to help out. The two of them then wake up fully healed and ready to leave. They both teleport out of the room to their destinations. Professor Oak returns to see the room empty. 

Shadow Mewtwo wakes up and tells his master that Mewtwo will head here soon. Giovanni orders Team Rocket to turn the lab into a fortress, Mewtwo is coming and they need to put an end to all of this once and for all.

Mewtwo returns to Zachary’s house and warns him and his Pokemon that there is another Mewtwo out there and this one works for Team Rocket. Unless this dark Mewtwo is defeated, it could mean world domination for Team Rocket at best, the end of the world at worst. The Pokemon there agree that this has to stop, they will handle Team Rocket while he focuses on the other Mewtwo. He then tells them about Mew and he is bringing some Pokemon with him as well. After hearing this, Zachary now wants to go just to see Mew. And with that, Mewtwo has his Pokemon ready to go. End of part 9.

Part 10 opens with Mewtwo and his crew of pokemon and Zachary hovering over the island where he was created. The place has the doors barricaded, the windows blocked and there is a portal of police boats blocking the island from all sides. On one of these boats has Officer Jenny and Xavier the Alakazam who took all available police to the island, but stopped here hoping to force Team Rocket to surrender by starving them out. Plus Xavier could feel Shadow Mewtwo’s energy and knew he and the police are no match for this monster.

Mewtwo sees Mew approaching from the west; with him are Articuno, Zapdos, Moltres, Lugia, and Ho-oh. The Five Legendary Birds have joined the fight. Mewtwo is impressed with Mew but asked who is guarding the World Tree, Lugia answers saying she left the might Regigigas to guard it while they were gone. Mewtwo then gives the order to strike and the birds use their power to break holes in the walls. The battle has begun. Zachary’s Pokemon rush in and attack Team Rocket head-on. Team Rocket get their Pokemon out to fight, including Charizard, Blastoise, and Venasaur: the same that defeated Mewtwo before. Charizard flies up and charges straight at Mewtwo. He uses his psychic powers for his best attack, one he learned from Mew when they were mind-linked. He has all non-legendary Pokemon under his control and orders them to turn on their masters. Zachary stays on the back of Alexander while all of this is going on. Now it is man versus Pokemon inside the research center. Even Meowth betrays Jesse and James but saved by falling debris. Meowth moves on to attack more members of Team Rocket while Jesse and James are trapped in a room blocked by heavy debris. Giovanni has to put down his Persian after in attacked one of the scientists. Shadow Mewtwo waits in his chamber for his opponent to arrive. Mewtwo finds Butch and Cassidy trying to make a run for the shore but are burned alive by Moltres. After about thirty minutes of fighting, it goes quiet. Mewtwo orders all Pokemon to retreat outside and get treated for their injuries. Zachary, Caila, and Erica heal the injured while Mewtwo goes looking for Giovanni. Some Team Rocket members did escape the battle only to be picked up by police boats and arrested on the spot. 

Eventually, Mewtwo finds the chamber where Shadow Mewtwo is there waiting for him. Mewtwo tries to explain to his double that he was used as a puppet for Giovanni and he treated poorly. Shadow Mewtwo knows what Mewtwo is trying to do but is not listening to him. Shadow Mewtwo and Giovanni are bonded, the same way he and Amber were bonded. It is then that Giovanni releases the door and the fight begins. They break through the ceiling and take their fight to the sky. During their intense fight, Mewtwo is knocked back to the island. The birds then go in for the attack, but Shadow Mewtwo is too fast and powerful for the five of them. Mew uses his power to revive Mewtwo. But before Mewtwo can get back into the fight, Zachary suggests that all Pokemon who can mega need to do so. He had upgraded his device to mega evolve all Pokemon at once rather than one at a time. He activates it and all Pokemon that can mega evolve on and around the island did including Charizard, Blastoise, Venasaur, Erica, Xavier, Victor, Caila, Mewtwo into his X form, and the Pokemon that were once fighting with Team Rocket like a Gengar, Sceptile, Blaziken, and Houndoom; but it also mega evolved Shadow Mewtwo as well into a black and orange X form. Mewtwo orders all Pokemon to hit Shadow Pokemon at once with their best range attacks. They all hit Shadow Mewtwo but to no effect. Shadow Mewtwo uses a shadow ball and vaporized Mega Gengar. Erica gets one good kick at the monster, but one punch from its first sends her flying toward Duke who catches her but the momentum sends them both to the sea where they land in the water just short of a police boat. Xavier uses his power to bring them onboard and fixes Erica’s broken jaw.

Lexi and Nathan team up to do a double flame wheel, but they just bounce off the monster. Victor bone rushes the monster but is knocked back, Pokemon one after another try to land a hit and fail. In the chaos, Zachary tries to add a Z Crystal into his device, but Shadow Mewtwo breaks the device and his arm at the same time. This causes all but the Mewtwos to devolve back to their original forms. Shadow Mewtwo demands everyone to kneel to the new God of this world. Lexi goes into full rage and charges at Shadow Mewtwo landing in a good clean hit, sending him into the wall. Victor and Caila go to check on Zachary. He offers Victor a Fightium Z Crystal and Mewtwo the Mega Stone. He then orders the two Pokemon to trust each and fight as one. Caila stays with Zachery while Mewtwo and Victor prepare to fight. They shake hands with the items together, unaware that they caused a chain reaction that caused the Z Crystal, the Mega Stone, Mewtwo, and Victor to fuse in a bright flash of light. Mewtwo and Victor have become a brand new Pokemon called Mewtario. Shadow Mewtwo comes back to see its newest challenger. The two fight in the air and it causes the weather to react violently during the battle.

Mewtario than goes full power and becomes Mega Mewtario. But Shadow Mewtwo is still a tough opponent, and it gets one clean hit at Mewtario, sending him into the lab and crashes into a room full of trapped Dittos. Mewtario lets them free and asks them to transform into him. They do so and now Shadow Mewtwo has to fight an army of Mega Mewtario. Shadow Mewtwo doesn't stand a chance and is beaten back on the island and knocked unconscious. Mewtario then grabs both nerve cords and rips them right out of Shadow Mewtwo ’s head, killing it and ending the fight.

Mewtario then glows white before splitting back into Mewtwo and Victor. Everyone is left speechless by what just happened. On the ground is a strange rock that the Z crystal and Mega Stone fused as, it is hot to the touch. Lexi grabs it and offers it to Zachary just as Mewtwo goes back to the lab to find Giovanni. By now the lab is falling apart with debris and the bodies of humans and Pokemon alike everywhere. Then Mewtwo hears a noise that gets him an agonizing headache. Giovanni emerges from the shadows with a sonic device in one hand and a gun in the other. Mew hears the cries and goes to help, only to be stopped by the device Giovanni is using. Just as he is about to pull the trigger, Persian comes back and bites the hand that has the device. Giovanni shoots Persian in the head, killing his own cat for good. But now the device is broken and Mewtwo wastes no time putting Giovanni in a stasis hold. He then uses his psychic powers to break Giovanni’s gun and now nothing will stop Mewtwo from ending it all. Mew asks to read the mind of Giovanni before he dies just to see if there was even the slightest hint of good left in him; he finds none. He sees hundreds of children longing for home, Pokemon longing to be free, countless numbers of dollars stolen, and so many lives ruined, and no care was given by Giovanni. Mewtwo was right, some humans are so far gone they are not worth saving. Better that one evil man dies than to have so many people suffer because of it. Mew leaves heartbroken knowing that such evil exists. He will not save Giovanni this time.

Giovanni dies very slowly and painfully by Mewtwo, the screams can be heard all the way to the boats where Erica listens with rejoice to know that it is finally over. As Mewtwo leaves the lab, he hears two people cry for help. He moves the debris out of the way to find Jesse and James still alive and very scared. Mewtwo holds the lifeless corpse of Giovanni and begs for their lives. Mewtwo is done killing, he promises to spare their lives only if they turn themselves in. They surrendered without a fight. Everyone leaves the island, the police have all of the surviving members of Team Rocket and the body of Giovanni. Mewtwo then uses his power to destroy the island. The Dittos transform into various Pokemon and go their separate say for one who transformed into a cast for Zachary. Mewtwo had won, but he still feels empty inside, as if there was more to be done. End of part 10.

The Finale opens in Pallet Town where Mewtwo and his Pokemon are given heroes welcome. It is a massive celebration that Beth and Tommy hosted for their heroes. The Governor gives Mewtwo and his Pokemon a full pardon while Zachary is given an opportunity to be the new Viridian City Gym leader once the gym has been rebuilt. Mewtwo says he could rebuild it and asks something that shocks everyone: he asks Zachary to adopt him and the Pokemon he calls family. Zachary agrees. 

The next day, Mewtwo uses his power to the turn the crater that was the Viridian City Gym in a brand new gym and house for Zachary. Meanwhile, Jesse and James tell the police everything they have done in the past and all the remaining hideouts of Team Rocket. As a result, their punishment was reduced to 1000 hours of community service rather than life behind bars, and all Pokemon that were originally theirs they got to keep and could gladly battle other trainers while performing their duties. 

A few days later, Lillie and Gladion became the first traveling trainers to challenge Zachary at his new gym. They came to do battle for the badge and wish to offer Mewtwo a sincere apology. Mewtwo accepts the apology, then Gladion summons out Silvally while Lillie brings out Alolan Ninetails. Mewtwo mega evolves into his X form and the fight can begin. 

Months pass by, it is winter in Pallet Town where Mewtwo and Lexi are looking at the graves of the Fuji Family. This is the first time he has been here ever and it is very emotional for him. He wishes he could see her again, Amber has not been visiting her in ghost form since Giovanni died. Without warning, Mew visits them and has an answer for him. Mew could feel Mewtwo ’s pain from the World Tree and wants to help him. Mew suggests that he visit the Shrine of Arceus in Sinnoh to seek closure. Arceus is the God of all Pokemon and therefore can do anything even commune with the dead. Mewtwo grabs Lexi and flies to Sinnoh with Mew leading the way. 

Once at the Shrine, Mew calls upon Arceus to arrive. This Pokemon is a holy deity, most mortals never get a chance to see such a divine being. Mewtwo came to see Amber one last time and that is all he asks of the Pokemon God. Arceus does more than bring Amber to him, Emily and another human all in angel form appear before Mewtwo and Lexi. Lexi rushes over to hug Emily and they embrace. Mewtwo is stunned that not only is Amber an angel, but she's also an adult angel. Amber tells Mewtwo that she, Emily, and Simon are guardian angels now. Lexi looks around for him but does see the Chandelure anywhere. The male angel identifies himself as Simon. In life, he was a Pokemon breeder who was murdered by his own family and possessed a candle and became a Litwick. Simon was the only thing he remembered and stuck with all the time he was a ghost Pokemon. 

Arcues gives Mewtwo a commandment to never kill again or else he will never see Amber in the afterlife, he swears to the God of all Pokemon. Amber whispers something shocking into Mewtwo’s ear and tells him he has to do it out of trust. Mewtwo hesitates at first but promises her he will do as he is asked of. Then the angels leave with Arceus back to the heavens. Mew heads back to the World Tree and Mewtwo takes Lexi back home. He tells no one what Amber told him. 

The next night, Mewtwo looks at the city skyline with Lexi. He then looks at her as if he is never going to see her again. He leans in for a kiss and she goes for it. Mewtwo then grabs the back of her head and uses his psychic powers on her. He has replaced all memories of them as a couple and instead made seek like Nathan was always her lover. After they are done kissing, Lexi opens her eyes like she woke up. She asks Mewtwo where Nathan is just as he arrives. Lexi runs at him hugs him right. Mewtwo gives Nathan a gesture that indicates that he should just go with it, which he does. Nathan and Lexi are now a couple. As soon as they leave, that is when Mewtwo breaks down. Amber appears and tells Mewtwo that everything will be okay. Mewtwo tries his best to trust her again but does know how things can be better without Lexi. 

The next day, Professor Oak arrives at the gym to see Mewtwo in private. He finds him and leads him to the parking lot. There Mewtwo sees someone truly beautiful to his eyes. In front of him is a Pokemon that looks like a female version of him. Her name is Mewthree and she is anxious to meet Mewtwo for the first time. Professor Oak and Dr. Fuji were secretly working on her to be a companion for Mewtwo just in case he outlived everyone and wouldn't have to live life alone. But Mewtwo is too starstruck to pay any attention to him. He holds Mewthree in his arms and the two of them share a mind link. He notices that she sounds a lot like Amber and asks her if it was okay if she wouldn't be being called Amber. To which she agrees. After their mind link, they know each other like a married couple, Amber breaks down and cried on Mewtwo ’s shoulders after seeing all the terrible things that happened to him. He holds her right and tells her that he is better with her. He got Amber back, and he is never going to leave her side. 

As the credits roll, there are photos of Amber and Mewtwo going site seeing, getting a house, Amber being pregnant, Duke and Erica adopting a Machop and Buneary, Nathan and Lexi having twin Chimchar together, Ash winning the world tournament with Mewtwo in the background, Jesse, James, and their Pokemon getting jobs as breeders, and Amber holding a baby Mewtwo with a green belly and tail. The post-credit scene is Amber and Mewtwo tucking their child in for the night. They head to the gym alone. Mewtwo tells Amber that they need to be ready for any and all threats to their family. So they are going to train. Mewtwo transforms into his X form while Amber evolved into her Y form. Then they spar off. The story ends as two Pokemon train for a battle they don't know when it will come. 

THE END.


End file.
